The performance of a single cell direct methanol fuel cell (DMFC) is optimized by evaluating the effect of the catalyst distribution in the membrane electrode assembly (MEA) via a 3D multi-physics, multi component, two-phase, and not-isothermal model. The model is computed with Comsol Multiphysics v4.4 platform, with a finite element analysis solver and simulation software. It consists of Maxwell-Stefan, Stokes-Brinckman, extended two-phase Darcy Law, modified Butler-Volmer and Tafel equations to simulate the performance of the DMFC, and to evaluate the electrochemical, fluid-dynamics and thermal phenomena. The use of a 3D model considering porous equation such as Stokes-Brinkman is helpful for understanding, describing the motions and hydrodynamic forces of interacting particles in Stokes flow, which is more realistic regarding catalyst description and validation. Moreover, the model can be used for evaluating intrinsic parameters of novel electrocatalysts. The model is validated against a set of experimental data, showing congruent and convergent data for a commercial 25 cm(2) MEA consisting of Nafion (R) 117 and electrodes (Pt/C at the cathode and Pt:Ru at the anode) at different temperatures and inlet methanol concentrations, confirming the accuracy of the model and the equations applied. The model is used to optimize the catalytic layer distribution to obtain a more uniform current density distribution along the anodic catalyst-membrane interface and a better cell performance. The optimized anodic catalytic distribution has been implemented in a 25 cm(2) in-house three-layer MEA and experimentally tested, included a short durability of 26 h, showing better stability compared to a MEA with a classic homogenous catalyst loading distribution. (C) 2017 Elsevier B.V. All rights reserved.